There is an increasing demand for high throughput and parallel nano-fabrication techniques. In particular, there is a high demand for a low-cost process capable of producing highly uniform arrays of nano-pillar and nano-holes, since these patterns have found wide range of applications in many devices such as solar cells, photodetector, surface plasmonics, photonic crystals, memory devices, nano-filtration, fuel cells, and artificial kidneys. Conventional photolithography techniques cannot satisfy the small dimension requirements in many of these applications, due to the light source's wavelength limit1. Techniques such as x-ray, electron-beam, focused ion beam and nano-imprint lithography can achieve the desired resolution, but are either slow or expensive for fabrication over large areas. Nanosphere lithography (NSL) is an approach that uses planar arrays of micro/nanospheres as a lithography mask to generate nano-scale arrays on the substrate. However, there are several limitations associated with this method. First is that the monolayer of spheres can always contain dislocations resulting in agglomerations of particles after metal evaporation and prevent successful lift-off. Second, the size and spacing of the holes are coupled, and hence these properties cannot be independently controlled. Finally, NSL requires spheres to be formed directly on the substrate surface, which is not possible for many materials.